Hello Surita,
1a
you can use Image>Stacks>3D Project to create a stack with a rotating 3d
view. You can save the result stack as avi, quicktime
or animated-gif.
1b
Yes if you save a stack as avi, quicktime or animated gif you get a film
with the slice animation.
2
I might not know the best methods to do this.
To measure a volume you can use the Measure Stack plugin from Bob Dougherty:
http://www.optinav.com/MeasureStack.htmYou draw a ROI on key slices and the ROI is interpolated for the slices
in between (taking into account only the form of the ROI, not the
pixel-values in the image).
If you have the same ROI on the first and last slice the ROI will be the
same for all slices in between, as well.
The plugin will measure each slice as well as the volume.
You could then inverse the selection and fill or clear the outside and
use for example the 3D Project again.
2a
You can use any available way to define the ROI in 2, for example
threshold and wand tool together.
All this is possible and works fine for not too complicated cases.
However to do data extraction for more complicated
3d modeling it is not really apt.
I'm just working on a tool for this, that should be available in about 2
weeks.
There is an incomplete version at
http://www.mri.cnrs.fr/mriwiki/uploads/download-mri-cia.htmBut this comes as a full system, including imagej at the moment. I'll
create a version as ImageJ plugin soon.
There also is the TrackEM2 plugin from Albert Cardona, that might help you:
http://imagejdocu.tudor.lu/imagej-documenation-wiki/plugins/trakem2Cheers,
Volker
Surita Banwait a écrit :
> Hi There
>
>
>
> I wanted to thank everyone for all of their helpful hints. I had a few
> more questions though:
>
>
>
> 1. can imageJ create an animation of a z stack (volume rotating)
> other than cycling through each slice?
>
> a. If so, how to save it?
> b. For slice animation as well, once it is created do I
> just save as .mpeg/.avi?
>
> 2. is there a way to draw a structure through out a z stack (ie
> make a circle all the way through a stack) and then render a 3D object
> from it and get volume measurements?
>
> a. Any other options for volume measurements, for example
> of a structure within a cell (labeled using IF)?
>
>
>
>
>
> Cheers,
>
> -Surita
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Surita Banwait
>
> Morphology & Imaging Core
>
> Buck Institute for Age Research
>
> 8001 Redwood Blvd.
>
> Novato, CA 94945
>
>
[hidden email]
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
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